Re: [Freesurfer] white matter parcellation of Brodmann areas

[Vinny K]

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Thank you very much!

On Wed., Feb. 10, 2021, 10:05 a.m. Douglas N. Greve, 
wrote:

> Use mris_anatomical_stats to create an LUT with the -c option. You can
> look in recon-all.cmd for an example. You only need to do one hemi as they
> both will be the same.
> There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and
> rh WM. For each one, you replicate the LUT created above but change the
> index number (first column) by adding a constant: 1000, 2000, 3000, 4000.
> You can also change the name to indicate the hemi and tissue type. Look in
> $FREESURFER_HOME/FreeSurferColorLUT.txt
> for how it works for the aparc+aseg.mgz and the wmparc.mgz. You can embed
> the LUT in the file itself with
> mri_convert file.mgz --ctab yournewLUT file.mgz
>
>
>
> On 2/9/2021 5:30 PM, Vinny K wrote:
>
> External Email - Use Caution
> Thanks Doug, the commands gave the expected outputs.  I used the original
> lh and rh BA_exvivo annotations and got the new BA+aseg.mgz and wmBA.mgz
> files.  Yes, please let me know how to proceed with the new LUT.
>
>
>
>
>
> On Tue, Feb 9, 2021 at 10:47 AM Douglas N. Greve 
> wrote:
>
>> Look in the subject/scripts/recon-all.cmd file of one of your subjects.
>> You will find five mri_surf2volseg commands
>> Use the 2nd one (the one that creates aparc+aseg.mgz) as your template
>> and modify it to take your BA annotation and output a "BA+aseg.mgz"
>> Use the last one ( the one that creates wmparc.mgz) as your template to
>> create your new wmBA.mgz file, modifying it as needed.
>> You will need to create a new LUT, but let's do that when you get there
>>
>> On 2/9/2021 10:26 AM, Vinny K wrote:
>>
>> External Email - Use Caution
>> I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
>>
>> On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve 
>> wrote:
>>
>>> which version of FS are you using?
>>>
>>> On 2/5/2021 10:02 PM, Vinny K wrote:
>>>
>>> External Email - Use Caution
>>> Hello,
>>>
>>> I'd like to obtain white matter parcellations of the Brodmann areas.  I
>>> am not certain that the generated wmparc file from recon-all has this type
>>> of parcellation.  I was able to convert Brodmann area label files to mgz
>>> format using mris_label2annot and mri_aparc2aseg commands.  How can I
>>> obtain white matter parcellation of the individual Brodmann area volumes?
>>>
>>> Thanks,
>>>
>>> Vinny
>>>
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>>> 
>>>
>>>
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>>
>>
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Re: [Freesurfer] white matter parcellation of Brodmann areas

[Douglas N. Greve]

Use mris_anatomical_stats to create an LUT with the -c option. You can 
look in recon-all.cmd for an example. You only need to do one hemi as 
they both will be the same.
There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and 
rh WM. For each one, you replicate the LUT created above but change the 
index number (first column) by adding a constant: 1000, 2000, 3000, 
4000. You can also change the name to indicate the hemi and tissue type. 
Look in  $FREESURFER_HOME/FreeSurferColorLUT.txt
for how it works for the aparc+aseg.mgz and the wmparc.mgz. You can 
embed the LUT in the file itself with

mri_convert file.mgz --ctab yournewLUT file.mgz



On 2/9/2021 5:30 PM, Vinny K wrote:


External Email - Use Caution

Thanks Doug, the commands gave the expected outputs.  I used the 
original lh and rh BA_exvivo annotations and got the new BA+aseg.mgz 
and wmBA.mgz files.  Yes, please let me know how to proceed with the 
new LUT.






On Tue, Feb 9, 2021 at 10:47 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Look in the subject/scripts/recon-all.cmd file of one of your
subjects.
You will find five mri_surf2volseg commands
Use the 2nd one (the one that creates aparc+aseg.mgz) as your
template and modify it to take your BA annotation and output a
"BA+aseg.mgz"
Use the last one ( the one that creates wmparc.mgz) as your
template to create your new wmBA.mgz file, modifying it as needed.
You will need to create a new LUT, but let's do that when you get
there

On 2/9/2021 10:26 AM, Vinny K wrote:


External Email - Use Caution

I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

which version of FS are you using?

On 2/5/2021 10:02 PM, Vinny K wrote:


External Email - Use Caution

Hello,

I'd like to obtain white matter parcellations of
the Brodmann areas.  I am not certain that the generated
wmparc file from recon-all has this type of parcellation. I
was able to convert Brodmann area label files to mgz format
using mris_label2annot and mri_aparc2aseg commands.  How can
I obtain white matter parcellation of the individual
Brodmann area volumes?

Thanks,

Vinny

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Re: [Freesurfer] white matter parcellation of Brodmann areas

[Vinny K]

External Email - Use Caution

Thanks Doug, the commands gave the expected outputs.  I used the original
lh and rh BA_exvivo annotations and got the new BA+aseg.mgz and wmBA.mgz
files.  Yes, please let me know how to proceed with the new LUT.





On Tue, Feb 9, 2021 at 10:47 AM Douglas N. Greve 
wrote:

> Look in the subject/scripts/recon-all.cmd file of one of your subjects.
> You will find five mri_surf2volseg commands
> Use the 2nd one (the one that creates aparc+aseg.mgz) as your template and
> modify it to take your BA annotation and output a "BA+aseg.mgz"
> Use the last one ( the one that creates wmparc.mgz) as your template to
> create your new wmBA.mgz file, modifying it as needed.
> You will need to create a new LUT, but let's do that when you get there
>
> On 2/9/2021 10:26 AM, Vinny K wrote:
>
> External Email - Use Caution
> I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
>
> On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve 
> wrote:
>
>> which version of FS are you using?
>>
>> On 2/5/2021 10:02 PM, Vinny K wrote:
>>
>> External Email - Use Caution
>> Hello,
>>
>> I'd like to obtain white matter parcellations of the Brodmann areas.  I
>> am not certain that the generated wmparc file from recon-all has this type
>> of parcellation.  I was able to convert Brodmann area label files to mgz
>> format using mris_label2annot and mri_aparc2aseg commands.  How can I
>> obtain white matter parcellation of the individual Brodmann area volumes?
>>
>> Thanks,
>>
>> Vinny
>>
>> ___
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>> 
>>
>>
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>
>
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Re: [Freesurfer] white matter parcellation of Brodmann areas

[Douglas N. Greve]

Look in the subject/scripts/recon-all.cmd file of one of your subjects.
You will find five mri_surf2volseg commands
Use the 2nd one (the one that creates aparc+aseg.mgz) as your template 
and modify it to take your BA annotation and output a "BA+aseg.mgz"
Use the last one ( the one that creates wmparc.mgz) as your template to 
create your new wmBA.mgz file, modifying it as needed.

You will need to create a new LUT, but let's do that when you get there

On 2/9/2021 10:26 AM, Vinny K wrote:


External Email - Use Caution

I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


which version of FS are you using?

On 2/5/2021 10:02 PM, Vinny K wrote:


External Email - Use Caution

Hello,

I'd like to obtain white matter parcellations of the Brodmann
areas.  I am not certain that the generated wmparc file
from recon-all has this type of parcellation.  I was able to
convert Brodmann area label files to mgz format using
mris_label2annot and mri_aparc2aseg commands.  How can I obtain
white matter parcellation of the individual Brodmann area volumes?

Thanks,

Vinny

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Re: [Freesurfer] white matter parcellation of Brodmann areas

[Vinny K]

External Email - Use Caution

I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve 
wrote:

> which version of FS are you using?
>
> On 2/5/2021 10:02 PM, Vinny K wrote:
>
> External Email - Use Caution
> Hello,
>
> I'd like to obtain white matter parcellations of the Brodmann areas.  I am
> not certain that the generated wmparc file from recon-all has this type of
> parcellation.  I was able to convert Brodmann area label files to mgz
> format using mris_label2annot and mri_aparc2aseg commands.  How can I
> obtain white matter parcellation of the individual Brodmann area volumes?
>
> Thanks,
>
> Vinny
>
> ___
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>
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Re: [Freesurfer] white matter parcellation of Brodmann areas

[Douglas N. Greve]

which version of FS are you using?

On 2/5/2021 10:02 PM, Vinny K wrote:


External Email - Use Caution

Hello,

I'd like to obtain white matter parcellations of the Brodmann areas.  
I am not certain that the generated wmparc file from recon-all has 
this type of parcellation.  I was able to convert Brodmann area label 
files to mgz format using mris_label2annot and mri_aparc2aseg 
commands.  How can I obtain white matter parcellation of the 
individual Brodmann area volumes?


Thanks,

Vinny

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[Freesurfer] white matter parcellation of Brodmann areas

[Vinny K]

External Email - Use Caution

Hello,

I'd like to obtain white matter parcellations of the Brodmann areas.  I am
not certain that the generated wmparc file from recon-all has this type of
parcellation.  I was able to convert Brodmann area label files to mgz
format using mris_label2annot and mri_aparc2aseg commands.  How can I
obtain white matter parcellation of the individual Brodmann area volumes?

Thanks,

Vinny
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Re: [Freesurfer] White matter parcellation

[Graterol Pérez , José Alberto]

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Hey, Douglas. Thanks for the answer and the references.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, February 2, 2021 5:57:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter parcellation

The subcortical GM structures are obtained from the whole brain segmentation 
(Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the 
label of the closest point on cortex (Salat, Neuroimage, 2009)




On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:

External Email - Use Caution

Dear FreeSurfer experts,

I need help trying to understand how the white matter gets parcellated. I have 
a clinical dataset, which means that the resolution is not as research images, 
but it ran without a problem. I would like to measure the volume of the basal 
ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a 
structure ends and the other one begins. I am attaching two images to show what 
I mean.

I would really appreciate some clarification. I am using FreeSurfer 7.1.1

Thanks in advance.
José




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Gerichtsstand: Hamburg | MailScanner has detected a possible fraud attempt from 
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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel



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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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Re: [Freesurfer] White matter parcellation

[Douglas N. Greve]

The subcortical GM structures are obtained from the whole brain 
segmentation (Fischl, Neuron, 2002). The segmentation of the WM is 
performed by taking the label of the closest point on cortex (Salat, 
Neuroimage, 2009)





On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I need help trying to understand how the white matter gets 
parcellated. I have a clinical dataset, which means that the 
resolution is not as research images, but it ran without a problem. I 
would like to measure the volume of the basal ganglia and looking at 
wmparc.mgz I am not sure how Freesurfer decides where a structure ends 
and the other one begins. I am attaching two images to show what I mean.


I would really appreciate some clarification. I am using FreeSurfer 7.1.1

Thanks in advance.
José




Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
Rechts; Gerichtsstand: Hamburg | *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* www.uke.de 

Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim 
Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel




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[Freesurfer] White matter Parcellation

[Graterol Pérez , José Alberto]

External Email - Use Caution

Dear FreeSurfer experts,

I need help trying to understand how the white matter gets parcellated. I have 
a clinical dataset, which means that the resolution is not as research images, 
but it ran without a problem. I would like to measure the volume of the basal 
ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a 
structure ends and the other one begins, because the structures are not really 
visible. I could upload two screenshots to show what I mean.

I would really appreciate some clarification. I am using FreeSurfer 7.1.1

Thanks in advance.
José
--

_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg | 
http://secure-web.cisco.com/1fL7_mV1HnVXx_pK-xzWgX0hp1IPRmxfnHHvyPV6axEvIN99tKLL4rqVW9pToIfDKy-D5Sm_-qItiTvmXlbn20AApfGepiSNRG9HD4nVqJXgD2cpm1eNEqG4CGCFXEMMHwAWOIZcxSELKpiTvtfJQqS11pDN-V6wawnKdKEd7q709fQspMZAmdsiRbiCBZeGtu7JWmdef5KX1_1XQUkedRDCAP2g8fHkjXOPFtXvENEUlMlNELzQjB3No_u-xwYGRwzkYNZorfNaylUj_2e3WKw/http%3A%2F%2Fwww.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
_

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[Freesurfer] White matter parcellation based on ROIs from fMRI

[Beyh, Ahmad]

Hello Freesurfers,

I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s. 
I want to use the ROIs for tractography, and therefore need them to include the 
underlying white matter.


I I am aware that freesurfer can do this after running the subjects through 
recon-all using freesurfer's own atlas. But is there a way to do this using the 
cortical ROIs defined in native space? So can I give freesurfer the T1 and the 
cortical ROIs as input and get the volumetric ROIs (that include white matter) 
as output in each subject's native space? This is important because the ROIs 
come from fMRI and are not based on the anatomy.


A detailed answer would be highly appreciated.

Many thanks,

Ahmad
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Re: [Freesurfer] white matter parcellation

[Bruce Fischl]

Hi Laurena

it doesn't use tensor fitting at all.

cheers
Bruce
On Mon, 4 Apr 2016, Holleran, Laurena 
wrote:



Thanks Bruce,

I have not used TRACULA before but I'll look into it. Does the tensor 
estimation have to be carried out using dtirecon for TRACULA or can I input 
tensor calculations from another software?

Thanks

Laurena

From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> 
on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Sent: 04 April 2016 15:45
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter parcellation

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?

cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena
wrote:



Hello experts,


I wanted to know if there are any other white matter parcellation methods
being developed which specifically label white matter tracts? I know that
the wmparc voxel are assigned a label based on the piece of cortex that is
closest too it​, however a significant portion of the white matter remains
unclassified or "unknown". If there are no plans to develop an atlas of this
sort you can just let me know.


Many thanks.







The materials in this message are private and may contain Protected
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in error, please immediately notify the sender via telephone or return mail.






The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
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Re: [Freesurfer] white matter parcellation

[Holleran, Laurena]

Thanks Bruce,

I have not used TRACULA before but I'll look into it. Does the tensor 
estimation have to be carried out using dtirecon for TRACULA or can I input 
tensor calculations from another software?

Thanks

Laurena

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: 04 April 2016 15:45
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter parcellation

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?

cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena
wrote:

>
> Hello experts,
>
>
> I wanted to know if there are any other white matter parcellation methods
> being developed which specifically label white matter tracts? I know that
> the wmparc voxel are assigned a label based on the piece of cortex that is
> closest too it​, however a significant portion of the white matter remains
> unclassified or "unknown". If there are no plans to develop an atlas of this
> sort you can just let me know.
>
>
> Many thanks.
>
>
>
>
> 
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
>
>


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] white matter parcellation

[Bruce Fischl]

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you 
might be able to run it without (which would amount to mapping the tracts 
from the atlas onto your individual subject). Perhaps Anastasia can 
comment?


cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena 
wrote:




Hello experts, 


I wanted to know if there are any other white matter parcellation methods
being developed which specifically label white matter tracts? I know that
the wmparc voxel are assigned a label based on the piece of cortex that is
closest too it​, however a significant portion of the white matter remains
unclassified or "unknown". If there are no plans to develop an atlas of this
sort you can just let me know. 


Many thanks.

 





The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you
are not the intended recipient, be advised that any unauthorized use,
disclosure, copying or the taking of any action in reliance on the contents
of this information is strictly prohibited. If you have received this email
in error, please immediately notify the sender via telephone or return mail.


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] white matter parcellation

[Holleran, Laurena]

Hello experts, 



I wanted to know if there are any other white matter parcellation methods being developed which specifically label white matter tracts? I know that the wmparc voxel are assigned a label based on the
 piece of cortex that is closest too it​, however a significant portion of the white matter remains unclassified or "unknown". If there are no plans to develop an atlas of this sort you can just let me know. 


Many thanks.



 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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[Freesurfer] White Matter Parcellation

[James Porter]

Hello-

In September of 2006 there was a post in which you mentioned that white 
matter parcellations were being fine-tuned but not yet ready. I'm really 
hoping to take advantage of the 3000 and 4000 level labels shown in 
FreeSurferColorLUT.txt, but I don't have them in my current 
parcellations that were created using FreeSurfer v3.0.3. Are there 
versions of the parcellation schemes available that I can upgrade to in 
order to obtain these finer white matter parcellations?


Thanks,

Jim Porter
TRiCAM Lab Coordinator
Elliott Hall N437
612.624.3892
www.psych.umn.edu/research/tricam
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Re: [Freesurfer] White Matter Parcellation

[Bruce Fischl]

Hi James,

we're hoping to release it along with a bunch of other things sometime 
this summer.


cheers,
Bruce
On Fri, 25 May 2007, James Porter wrote:


Hello-

In September of 2006 there was a post in which you mentioned that white 
matter parcellations were being fine-tuned but not yet ready. I'm really 
hoping to take advantage of the 3000 and 4000 level labels shown in 
FreeSurferColorLUT.txt, but I don't have them in my current parcellations 
that were created using FreeSurfer v3.0.3. Are there versions of the 
parcellation schemes available that I can upgrade to in order to obtain these 
finer white matter parcellations?


Thanks,

Jim Porter
TRiCAM Lab Coordinator
Elliott Hall N437
612.624.3892
www.psych.umn.edu/research/tricam
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